Scientists find 34 different lineages of Covid-19 in Bengaluru

The genomic sequencing of 197 Covid-19 samples from foreign fliers arriving in Bengaluru and city residents has come up with some surprises.

Not only have researchers found 34 different lineages of the original Sars-CoV-2 in the city (up from the seven found in May 2020) but a majority of viruses in Bengaluru come from a lineage characterised by different mutations which allow the virus to evade a response from the human immune system.

At the same time, scientists found that there is no evidence to suggest that the much-feared UK variant of the virus was present in Karnataka until the arrival of foreign fliers in the third week of December.

The finding was made by researchers from Nimhans who analysed 75 samples from international fliers, 103 from city residents and 14 from an outbreak at a college of nursing in North Bengaluru in the middle of February. The study was conducted from November to February.

The B.1.36 lineage, which contains nine amino acid mutations associated with immune escape, comprises 43.7 per cent of the 103 samples processed from Covid-19 residents of the city. Out of these, analysis also found that 56.92 per cent of the B.1.36 samples includes the N440K mutation, which has been previously determined as being capable of causing reinfections.

Also read: Only 11,000 Covid-19 samples sequenced by INSACOG so far

“The immune escape associated with amino acid change, N440K, has been reported from the states of Andhra Pradesh, Maharashtra, Telangana and Karnataka, and is also associated with reinfection,” the researchers wrote in their study, which is currently in pre-press. They also found that the outbreak at the nursing college was driven by “related viruses belonging to the 1.36 cluster”.

According to the Bruhat Bengaluru Mahanagara Palike (BBMP), the nursing college’s index cases were recent arrivals from Kerala.

However, evidence that these immune escape variants are behind the surge is not yet proven. Noted epidemiologist Dr Giridhar Babu said that the N440K variant had been found in only 124 samples from 11 districts out of 2,032 samples from 14 districts in Kerala, which is also suffering a surge of cases. “The variant is found in 33 per cent of samples from Andhra Pradesh, and in 53 of 104 samples from Telangana. Yet these states didn’t report a surge in cases,” he tweeted.

In contrast, Maharashtra, which in the midst of a surge of cases had reported a fraction in the increase of samples with the E484Q and L452R “double” mutations, disclosed by the centre on Wednesday. The study also found that 24 out of 73 international fliers had the B.1.1.1.7 or the “UK variant” of the novel coronavirus, making this the major lineage imported into the state. Some 20 out of 73 fliers had the B.1.36 lineage.